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Neuroscience Basics

Bridging biochemical, structural, and behavioral sciences to understand people

by TAF Senior Intern Liz Chamiec-Case

The brain is just another organ, but how crazy is it that the part of our bodies and the part of science that we know the least about is the same part that controls everything we think, say, feel, and do? Because we know so little about the brain and how it works, it is not uncommon to have a dualistic view of ourselves: on the one hand we understand that the brain sits up there in the skull, helps coordinate the body’s functions, store memories, and regulates how we think and feel; while on the other hand, when we introspect “where am ‘I’?” we picture an out-of-body ethereal and separate existence. Again, the brain is just another organ – if there is anything abnormal about our memories, feelings, or behaviors, it is the result of abnormal brain chemistry or structure. In this section, we will explore some of the basic brain structures and functions, the nervous system, neurotransmitters and biochemistry, and briefly discuss emotions. It is our hope that a small amount of understanding will empower you to see that the brain is not so mystical, but rather just another organ that we need to take care of.

The Brain - Structure and Function

The brainstem is located at the top of the spinal cord; it connects the spinal cord and brain by relaying messages between the two. It also plays a major role in regulating the autonomic nervous system; this, as the name implies, is what regulates the automatic bodily functions that we really don’t want to have to think about (like breathing, heart rate, blood pressure, and digestion). At the core of the brainstem is a special group of brain cells (neurons) called the reticular formation and they control consciousness, breathing, the conveyance of sensory information, and motor control.

Spinal Cord
The spinal cord is a length of neural tissue that is enclosed in the vertebrae. Stretching from the lower back up to the brain, the spinal cord consists of segments of nerves with white and gray matter. With the purpose of meeting the most basic needs for survival, the brainstem has branches of nerves that diverge from the main cord and travel to muscles and organs throughout the body. One of the most prominent functions of the spinal cord is its involvement in the reflex arc; there, it receives signals from a harmful stimulus and creates a quick response to avoid danger- for example, when a hot surface is touched and the hand is jerked away.

Found at the top of the brainstem, the thalamus acts as a bridge and relay station for signals to be routed appropriately. To do this, it takes sensory signals and carries them to the the areas in the cerebral cortex that receive, interpret, and process these signals. The thalamus also acts in the opposite direction, meaning that it carries instructions for actions from the medulla and cerebellum to the brainstem to be dispersed throughout the body.

Cerebral Cortex
The cerebral cortex is the thin layer of neurons that covers the cerebrum by folding itself, giving the brain its telltale wrinkled appearance. Much of the cerebral cortex is gray matter and is therefore made up of the neurons themselves, as opposed to white matter which primarily represents the fatty insulating material around the signaling tail, or axons, of the neurons. The cerebral cortex is the site of communication and connection between neurons. In fact, the average brain has over 300 trillion such connections in this region, called synapses. The cerebral cortex plays a primary role in thinking, controlling perceptions, and consciousness.

Neocortex (AKA Cerebrum)
Making up about 85% of the brain’s weight, the cerebrum is by far the largest structure of the human brain. By achieving functions such as higher level thinking, decision making, and the ability to create and carry out plans, this region of the brain is said to be the cause of humanity. Because the cerebrum is such a large section of the brain, it is further split into four lobes (the frontal, occipital, temporal, and parietal lobes), and the cerebral cortex, a layer of neurons over the top. The regions of the cerebrum are responsible for sensory functions, motor functions, and association areas. While these lobes serve very specific, genetically encoded functions, it should be noted that the brain will not waste space. For example, if an individual is born blind (or even blinded at a young age) the neurons in the occipital lobe can be reused to perform a new function like language processing.

Occipital Lobe
Split into the primary visual cortex and the secondary visual cortex, the occipital lobe specializes in interpreting vision. The primary visual cortex serves to take information from the eyes and preserve the integrity of the image by keeping the proportion, space, and size accurate. The information is split so that everything on the left side of the image goes to the right hemisphere, activating neurons on the right side of the brain, and everything on the right side of the image goes to the left side of the brain, thus activating the neurons on the left. The secondary visual cortex consists of the neurons around the primary visual cortex and makes the image more specific by adding color and motion.

Temporal Lobe
If vision is a projection of what is physically around someone and hearing is an auditory depiction, the temporal lobe is what takes that basic information and makes it something that would register with knowledge or memory. For example, the fusiform face area is the part of the brain that recognizes faces whereas other parts of the temporal lobe recognize objects, landscapes, images, or other sights. The primary auditory cortex has primary and secondary auditory areas which process sounds, including an area on the left side of the brain that takes words and phrases that are heard and processes them to give them meaning. Once these visual and auditory stimuli are processed, the hippocampus and amygdala, both also located in the temporal lobe, stores them to memory so that the next time a similar sight or sound is seen or heard, connections can be made from the previous memory.

Frontal Lobe
The frontal lobe is the part of the brain that gives an adult their maturity. As a person grows, the frontal lobe develops to form organized circuits of neurons located behind the forehead. Behaviors that society expects of someone who is “mature” come from this region of the brain including the ability to concentrate, plan, and follow societal norms. One subregion is the prefrontal cortex, which hosts a large portion of the functions. For example, it is in charge of directing and maintaining attention while also blocking out background stimuli which may distract concentration. It causes the body to carry out plans that it created, and provides the basis for reception of actions based on empathy and social norms. The orbitofrontal cortex, located behind the eyes, helps define personality by playing a role in emotions and impulse control. Finally, the primary motor cortex causes physical action based on decisions made in the other regions of the frontal lobe by sending messages down the brainstem to the muscles.

Parietal Lobe
The parietal lobe controls the continuation of the touch and sight senses. Stimuli from touch receptors are connected to the brainstem; these stimuli send the message up to the primary somatosensory cortex, a strip of neurons that receive touch stimuli and run along the sides of the brain. Receptors on this cortex correspond to where the stimulus touches, and parts of the body that are physically close are likewise close on the somatosensory cortex. Collectively, the entire body is represented by the somatosensory homunculus, the ratio of amount of area dedicated to a particular region based on the level of sensitivity. For example, a sensitive area such as the lips would have more area than a less sensitive area, such as the leg. The other primary job of the parietal lobe is to establish spatial relationships. Although the eyes can create a projection of the objects around them, the parietal lobe is needed to process this and understand the concept of space that is open, space that is taken up, and the distance between objects.

Corpus Callosum
With the right hemisphere of the brain controlling the left side of the body and the left side of the brain controlling the right side of the body, a connection is needed to ensure communication between the two hemispheres. This connection is made by the corpus callosum, which consists of axon fibers that cross the space between the two hemispheres. Impulses can travel across the corpus callosum to allow the transport of information between the two sides of the brain.

The cerebellum is most commonly known as the part of the brain that enables balance and controlled motion. It is small, round, and extends off the back of the brainstem. In addition to coordinating movement, it houses certain cognitive processes that involve movement including planning, memory, and putting language into actions. Voluntary movement comes from collaboration with the pons to maintain balance and steadiness. The nervous system trains the cerebellum to work independently and without thought so that motion can be achieved while the brain is performing other tasks. Interestingly, all of the neurons throughout the cerebellum are identical, suggesting that all signals are identical, but the area that receives them is what differentiates the signals into different actions.

Limbic system
The limbic system is known as the animalistic part of the brain that functions to perform the basic needs for survival. Located between the hemispheres of the cerebrum, the system mainly consists of the amygdala and hypothalamus.

The hypothalamus is part of the animalistic section of the brain that is geared toward basic survival. Located just below the thalamus, the hypothalamus releases hormones to cause feelings according to what the body needs. For example, when glucose levels are low, a hormone will be released signaling that the person is hungry so that food will be eaten and glucose levels can return to normal. Other controls that are regulated include blood pressure, water levels, and temperature. In addition, the hypothalamus creates feelings of lust to drive reproduction so that the animal will produce offspring and pass on its genetics. The ability to regulate these functions comes from the ability of the hypothalamus to reward the body and through hormones, so that it can have control over what needs are met.

The hippocampus is the part of the brain in charge of creating and storing memories. Defined as connections between neural matter to form associations, memories are created by networks of neurons connecting via dendrites to enable the travel of impulses so that two ideas, objects, or events are linked and can easily trigger one another. In addition to memories of events, the hippocampus is responsible for remembering where places and objects are located, forming a direct connection to the sense of sight.

The amygdala works with the hypothalamus, hippocampus, and cerebral cortex to create connections that relate directly to emotions with an emphasis on fear. Physically just a pair of neural clusters that make up a part of the limbic system, the amygdala associates an event, object, or other stimulus with some emotion that goes with it. Evolutionarily, the connections that pertain to fear are especially important because of the use of fear to protect an animal from dangers to survival.

Basal Ganglia
The basal ganglia is a system made up of small structures located under the cerebral cortex with the purpose of assisting the thalamus by carrying information from the cerebral cortex to the motor centers of the brainstem. One of those structures is the nucleus accumbens, a collection of neurons that release dopamine when something pleasurable is seen. This is known as part of the reward system because dopamine, a neurotransmitter, brings what is identified as relief and positive feelings.

The Brain - The Nervous System

The nervous system plays a major part in the body’s function of moving, responding to stimuli, and maintaining homeostasis (a stable environment). It is a very general term and is broken down into the Central Nervous System (CNS) and the Peripheral Nervous System (PNS). The PNS is further broken down into the Autonomic and Somatic Nervous Systems, and the Autonomic system is divided into Sympathetic and Parasympathetic functions. All of these systems function differently but are interdependent to keep the body working properly. A commonality is the use of neurons to carry messages between parts of the system, providing the cell communication that makes the system so efficient. When all these factors work together, the body is in full communication with itself.

Central Nervous System
The central nervous system consists of the brain, the spinal cord, and the nerves that connect them. The structures are isolated by a blood-brain barrier, blood vessels that have small gaps to let only a few materials through as protection. The brain is the control center where all stimulus information goes to, and all instructions for movement or function come from. The spinal cord runs down the body and primarily collects messages from the neurons in the body to send them up to the brain. Its other use is the reflex arc, in which a stimulus that is labeled as dangerous, such as touching a hot stove, goes to the spinal cord. Without going up to the brain to save time and prevent further damage, the spinal cord sends a response back, causing a path to go from muscle to spinal cord to muscle.

Peripheral Nervous System
The Peripheral Nervous System is all of the nerves in the body not found in the spinal cord or brain. Most of these are found in the muscles or organs so that messages can be delivered to maintain function or stimulate movement. For example, the legs can get messages via the PNS to start walking or the heart can be stimulated to beat faster when running. The PNS is connected to the CNS by the spinal cord, so impulses are carried down and away from the brain and are then picked up by nerve cells of the PNS. From here, the PNS is further divided into the Autonomic and Somatic Nervous Systems.

Somatic vs Autonomic vs Enteric
The PNS is further divided into the somatic and autonomic nervous systems. The autonomic nervous system includes all of the subconscious actions and functions. For example, because you continuously breathe without telling your body to inhale and to bring in oxygen to go to your muscles and then exhale waste carbon dioxide, breathing is an autonomic function. Somatic functions are the opposite, meaning that they require a message from the brain to tell them to happen. For example, if you want to walk across the room, you control this movement with the direction from your brain, telling your muscles to move your legs and carry you across the room. The enteric nervous system consists of all parts of the gastrointestinal system, working to break down food into usable energy. It works independently of the other nervous systems, but it both influences and is influenced by the somatic and autonomic nervous systems.

Sympathetic and Parasympathetic
Part of the function of the autonomic system is to respond to stimuli that require action by the body. Specifically, the sympathetic system responds when there is a danger, sending the body into fight, flight, or freeze mode. Triggering the release of epinephrine (adrenaline) from the adrenal glands, the sympathetic system increases heart rate and breathing rate, contracts blood vessels, and stops digestion to put all available energy into the fight or flight response. This feeling is the rush of adrenaline you feel when someone jumps out from behind you or a car speeds past where you’re standing, almost hitting you. The body is preparing itself to fight a predator or run away as a method of survival. This response, however, takes a great deal of energy that the body cannot sustain for long amounts of time, so the parasympathetic system functions to release norepinephrine (noradrenaline) to return body levels to normal. Therefore, in the release of this hormone results in slowed breathing and heart rate, dilation of blood vessels, and the resumption of digestion.

The Neuron
All of the structures of the brain and nervous system are made up of neurons. The neuron is the type of cell that makes up the structures of the neurological system. The parts of the neuron include the dendrites, which receive signaling information; the cell body, that interprets signals and house the cell’s energy and production organelles; the axon, which sends signals out; and the synapse, the connecting space between two cells. The cell body is found at the center and contains the nucleus and organelles that control the cell. Protruding from one side is the network of dendrites, long strings that connect each neuron with up to 7,000 others and make the brain into one large circuit. Coming out of the other side of the cell body is the axon, a long strand covered in myelin that conducts impulses towards the next neuron. The synapse is found at the end of the axon and is the site where neurotransmitters are released and impulses leave the neuron. The synapse serves as the site of communication between cells. Three general types of neurons make up the system: motor neurons, sensory neurons, and interneurons. Motor neurons send instructions from the brain to muscles and organs to coordinate movement and organ functions. Sensory neurons travel from muscles to the brain via the spinal cord to deliver stimuli or other messages. However, motor and sensory neurons cannot directly interact, so interneurons have the job of delivering messages between the two.

Electrical Stimulation and Impulse Travel
Neurons at resting potential, meaning there is no impulse traveling across them, are negatively charged due to the number of positive protons outside the neuron. The difference between the negative inside and positive outside is what enables impulses to be carried down the neuron. When an impulse comes down the axon, it causes the neuron to fire and the cell is then  depolarized. The purpose of a neuron firing is to either carry the impulse and relay it to a connected neuron or to release neurotransmitter chemicals to cause a response. This way, impulses can quickly be carried along the circuits in the brain, enabling fast spread of information, and neurotransmitters can cause reactions to stimuli sent to the brain.

Once the neuron is depolarized, it must be polarized so that it can fire again. In order to do this, sodium-potassium pumps in and the cell membrane of the neurons start working to pump three sodium ions out of the cell for every two potassium ions pumped in. As a result, the neuron can return to its “relative” negative resting potential and can fire again when the next impulse comes.

The Brain - Biochemistry

Neurotransmitters are chemical messengers that signal throughout the brain. Stored in vesicles in terminal buttons at the end of axons, impulses go to these terminal buttons and signal the release of the neurotransmitters. From there, the neurotransmitters exit the neuron and are released into the space between the terminal junction of the releasing neuron and the dendrites of the next. Neurotransmitters then bind to the dendrites of the next neuron. Each neurotransmitter has a specific shape that corresponds with the shape of its receptor, allowing a lock-and-key fit. From there, responses can start. Drugs and toxins can have effects by mimicking the shape of the neurotransmitters and binding to the receptors, either mimicking the physiological response, blocking the expected response, or amplifying it. The signal is ended by reuptake of the neurotransmitters, in which the neurotransmitters are taken back into the pre-synaptic (axon) cell terminal; enzymatic deactivation, in which enzymes destroy the neurotransmitters; or autoreception, in which the amount of neurotransmitter released is controlled and the neuron can stop when the signal is no longer needed. Some examples of neurotransmitters include acetylcholine, epinephrine (also called adrenaline), norepinephrine, serotonin, and dopamine. Acetylcholine controls messages that go between neurons and muscles and causes the muscles to contract. Epinephrine and norepinephrine work together in situations when danger is detected to prepare the body for fight or flight and then restore it to normal function. Serotonin controls emotions and mood, and dopamine is known as the brain’s reward system.

White and Gray Matter
White and gray matter is named for the literal colors of the neurons seen in the brain. The white matter refers to myelin that coats the axons of neurons. The beads of fat that go down the axon to facilitate fast conducting of neurons are known as a myelin sheath. The gaps between the beads of myelin are known as Nodes of Ranvier, and the negative impulses cannot travel within the axon because of the polarity of the myelin. Therefore, the negative impulses jump from node to node, enabling faster travel than if they had to pass through the entire axon. Keeping in mind that the brain is full of circuits, myelin acts as the “rubber” of wires. The metal part of the wire, however, would be gray matter. Gray matter refers to the cell bodies and dendrites that form connections throughout the brain to make a network of circuits that connect all of the millions of neurons together, enabling messages to be sent to any part of the brain.


One thing to know about emotions is that it’s impossible to name an emotion and point to a single part of the brain that controls it. Instead, different aspects of different structures contribute, and the network of neurons that enables communication throughout the entire brain leads to what we call feelings. Another thing to know about emotions is that the physical changes can be named, the feeling can be subjectively described, and beliefs/understandings can contribute to how a situation is perceived, but in the end, there is no objective definition of happiness, sadness, or any other emotion.

Emotional Theories
Three theories make up current understandings of emotions: the James-Lange theory, the Cannon-Bard theory, and the Schachter-Singer two-factor theory. None have been disproven; however, the Cannon-Bard theory is most widely supported by scientists. The Cannon-Bard theory suggests that emotional feelings and physical reactions are two separate entities that come from different areas of the brain as the result of one stimulus. Since the feeling and the physical reaction are simultaneous, they are perceived as being together. The James-Lange theory says that actions are the cause of emotions. For example, when someone sees a spider, their heart rate increases, their pupils dilate, and their palms start to sweat. As a result of these physical changes, fear is the labeled emotion. The Schachter-Singer two-factor theory requires the viewing of the situation as a whole in which the combination of the physical response and the idea that a feeling, or emotional label, should come as a result, trigger the emotion.

Emotions in the Brain
Although no one part of the brain can be linked directly to a particular emotion, it is known that the amygdala is the receiving unit of sensory stimuli that trigger emotions, and the orbitofrontal cortex helps to distinguish them. Stimuli can take two paths to the amygdala: either they can go straight through the thalamus to the amygdala for almost instantaneous, surface-level associations, or they can go through the sensory cortex and then to the amygdala. This longer path allows for the stimulus to be better processed and evaluated. This way, the feeling has more meaning and can contribute to the making of memories by altering how the hippocampus receives it. Being part of the limbic system, the amygdala has a major role in the processing of stimuli, especially those that lead to fear. Emotions, depending on the stimulus, vary based on their level of intensity and the valence, or if they are labeled as pleasant or unpleasant. The amygdala specializes in identifying the intensity whereas the orbitofrontal cortex identifies the valence. Stimuli that present a danger are more likely to be more intense, meaning that the amygdala will have a stronger and faster reaction and emotion attached to it. These fears are often remembered because of the way it is presented to the hippocampus and the survival advantage in remembering situations that cause fear. Emotions with a high intensity are put into long-term storage by the hippocampus whereas those with lower intensity go to short term storage. From here, people can be conditioned to feel fear in response to a particular situation or stimulus by repeatedly presenting an image seemingly harmless and connecting a strong emotion, such as fear, with it. Because of the brain’s high capacity of storing emotions, the image will eventually be associated with fear, leading to the immediate triggering of the emotion in response to the image.


Many people attribute behavior with a mind, a soul, or a set of morals. For example, the saying “mind over matter” suggests that a mind controls how someone behaves and responds to a certain situation. If you think about it, though, where is the mind located? In the head? The heart? What is really dictating this behavior? According to science, there is no structure for a mind or a soul, leaving only the brain to control behaviors.

Chemicals Change Behaviors
Physical structures or changes in the brain dictate behavior. One way this happens is in the release of chemicals that result in certain feelings and therefore actions. For example, when the brain releases serotonin, the feeling that accompanies is labeled as “happiness.” As a result, you may smile, causing your eyes to squint, your cheeks to lift, and the sides of your mouth to wrinkle. On the other hand, lower levels of dopamine in the brain is labeled as “depression,” causing behaviors such as frowning, poor posture, and negative thoughts.

Structures Change Behaviors
Changes to the connectivity and biochemistry (i.e. the physical structures) in the brain dictate behavior. One way this happens is in the parts of the brain that control how your body responds to signals. For example, in a properly functioning body, the brain stem is an intermediate structure between the brain and the spinal cord that relays messages from muscles to brain and brain to muscles. For people whose brainstems are severed, this carrying of messages cannot occur. As a result, symptoms include a lack of ability to maintain a heartbeat, the need of a machine to carry out respiration, and eventually death as the body can no longer carry signals and perform basic functions. This is a very extreme example of a malfunction in a structure leading to a detrimental behavior.

Another famous example of neuro-circuitry regulating behavior is that of Phineas Gage. Gage worked building railroads by blasting apart masses of rock with dynamite. When the dynamite exploded early, the tamping stake he used to push it into the hole shot up and through his head, destroying a significant portion of his frontal cortex. Remarkably, Gage survived, but his behavior was affected because of the loss of function of the frontal cortex. Since that region of the brain is responsible for concentration, the ability to plan, and the ability to regulate impulses and recognize societal norms and social cues (we call this ‘executive function’), Gage appeared to have lost his ability to regulate his impulses, causing him to behave like a child with a short attention span, a major focus on the present without looking ahead, and impulsiveness causing an inability to follow societal norms.

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